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Yorodumi- PDB-3gv4: Crystal structure of human HDAC6 zinc finger domain and ubiquitin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gv4 | ||||||
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Title | Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG | ||||||
Components |
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Keywords | HYDROLASE / HDAC6 / zinc finger / ubiquitin C-terminal peptide RLRGG / SGC / Actin-binding / Chromatin regulator / Cytoplasm / Metal-binding / Nucleus / Phosphoprotein / Polymorphism / Repressor / Transcription / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement ...negative regulation of hydrogen peroxide metabolic process / cellular response to topologically incorrect protein / polyubiquitinated misfolded protein transport / positive regulation of cellular response to oxidative stress / erythrocyte enucleation / negative regulation of aggrephagy / positive regulation of cholangiocyte proliferation / response to misfolded protein / negative regulation of oxidoreductase activity / regulation of microtubule-based movement / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / negative regulation of protein-containing complex disassembly / protein-containing complex disassembly / negative regulation of axon extension involved in axon guidance / regulation of establishment of protein localization / positive regulation of tubulin deacetylation / tubulin deacetylation / regulation of autophagy of mitochondrion / Cilium Assembly / peptidyl-lysine deacetylation / tubulin deacetylase activity / collateral sprouting / Transcriptional regulation by RUNX2 / lysosome localization / misfolded protein binding / negative regulation of protein acetylation / negative regulation of microtubule depolymerization / ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / protein deacetylation / cilium disassembly / response to growth factor / dendritic spine morphogenesis / histone deacetylase / aggresome assembly / regulation of androgen receptor signaling pathway / protein lysine deacetylase activity / positive regulation of signaling receptor activity / cellular response to misfolded protein / positive regulation of dendrite morphogenesis / cellular response to parathyroid hormone stimulus / aggresome / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / regulation of fat cell differentiation / microtubule associated complex / histone deacetylase activity / response to corticosterone / dynein complex binding / negative regulation of gene expression, epigenetic / protein quality control for misfolded or incompletely synthesized proteins / positive regulation of epithelial cell migration / axonal transport of mitochondrion / Notch-HLH transcription pathway / response to dexamethasone / beta-tubulin binding / cell leading edge / RUNX2 regulates osteoblast differentiation / histone deacetylase complex / response to immobilization stress / polyubiquitin modification-dependent protein binding / cilium assembly / alpha-tubulin binding / HSF1 activation / regulation of macroautophagy / negative regulation of protein-containing complex assembly / positive regulation of synaptic transmission, glutamatergic / inclusion body / axon cytoplasm / response to amphetamine / multivesicular body / epigenetic regulation of gene expression / transcription corepressor binding / ciliary basal body / ubiquitin binding / regulation of autophagy / caveola / actin filament organization / negative regulation of proteolysis / intracellular protein transport / Late endosomal microautophagy / protein destabilization / Hsp90 protein binding / regulation of protein stability / tau protein binding / NOTCH1 Intracellular Domain Regulates Transcription / histone deacetylase binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / beta-catenin binding / autophagy / Aggrephagy / Chaperone Mediated Autophagy / cellular response to hydrogen peroxide / protein polyubiquitination / positive regulation of peptidyl-serine phosphorylation / actin binding / cellular response to heat / microtubule binding / perikaryon / microtubule / RNA polymerase II cis-regulatory region sequence-specific DNA binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Dong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. ...Dong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human HDAC6 zinc finger domain and ubiquitin C-terminal peptide RLRGG Authors: Dong, A. / Ravichandran, M. / Loppnau, P. / Li, Y. / MacKenzie, F. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Dhe-Paganon, S. / Min, J. / Ouyang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gv4.cif.gz | 39.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gv4.ent.gz | 25.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gv4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3gv4_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 3gv4_full_validation.pdf.gz | 436.5 KB | Display | |
Data in XML | 3gv4_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 3gv4_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/3gv4 ftp://data.pdbj.org/pub/pdb/validation_reports/gv/3gv4 | HTTPS FTP |
-Related structure data
Related structure data | 3c5kS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12023.739 Da / Num. of mol.: 1 / Fragment: UNP residues 1109-1215 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDAC6, KIAA0901, JM21 / Plasmid: P28A-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBN7, histone deacetylase | ||||
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#2: Protein/peptide | Mass: 559.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ubiquitin C-terminal peptide | ||||
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.12 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop Details: 20% PEG3350, 0.2 M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 14, 2008 / Details: VariMax HR |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→50 Å / Num. all: 10865 / Num. obs: 10865 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.72→1.78 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.231 / Mean I/σ(I) obs: 4.26 / Num. unique all: 813 / Rsym value: 0.231 / % possible all: 72.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3C5K Resolution: 1.72→33.45 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.51 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.125 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.958 Å2
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Refinement step | Cycle: LAST / Resolution: 1.72→33.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.762 Å / Total num. of bins used: 20
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